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Yorodumi- PDB-8ct0: Crystal structure of FAD reductase CtcQ from Kitasatospora aureof... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ct0 | ||||||
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Title | Crystal structure of FAD reductase CtcQ from Kitasatospora aureofaciens in complex with FAD and NAD | ||||||
Components | Flavin reductase (NADH) | ||||||
Keywords | FLAVOPROTEIN / Reductase / Chlortetracycline / FAD binding / Biosysthesis / Natural product | ||||||
Function / homology | Function and homology information flavin reductase (NADH) / flavin reductase (NADH) activity / FMN binding Similarity search - Function | ||||||
Biological species | Kitasatospora aureofaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Hou, C. / Tsodikov, O.V. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structures and complex formation of halogenase CtcP and FAD reductase CtcQ from the chlortetracycline biosynthetic pathway Authors: Hou, C. / Garneau-Tsodikova, S. / Tsodikov, O.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ct0.cif.gz | 281.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ct0.ent.gz | 229.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ct0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ct0_validation.pdf.gz | 9.1 MB | Display | wwPDB validaton report |
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Full document | 8ct0_full_validation.pdf.gz | 9.2 MB | Display | |
Data in XML | 8ct0_validation.xml.gz | 55.6 KB | Display | |
Data in CIF | 8ct0_validation.cif.gz | 73 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/8ct0 ftp://data.pdbj.org/pub/pdb/validation_reports/ct/8ct0 | HTTPS FTP |
-Related structure data
Related structure data | 7v0bC 7v0dC 4l82S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 20987.883 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: The C-terminal sequence LEHHHHHH is a C-terminal tag artifact. The residues are not present in the structure due to disorder. Source: (gene. exp.) Kitasatospora aureofaciens (bacteria) / Gene: ctcQ, B6264_18520, HS99_0013300 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S4S3E3, flavin reductase (NADH) |
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-Non-polymers , 5 types, 263 molecules
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-NAD / | #5: Chemical | ChemComp-NAI / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.92 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.6 M KH2PO4,0.6 M NaH2PO4, 0.1 M Tris pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 49072 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / CC1/2: 0.978 / Rmerge(I) obs: 0.138 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.568 / Num. unique obs: 2399 / CC1/2: 0.696 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4L82 Resolution: 2.45→34.97 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.877 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.112 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.59 Å2 / Biso mean: 21.327 Å2 / Biso min: 2.94 Å2
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Refinement step | Cycle: final / Resolution: 2.45→34.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.513 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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